BPS2026 – CATMD: Comprehensive analysis toolkit for molecular dynamics analysis

Despite breakthroughs in protein structure prediction, the next frontier in computational biology lies in understanding structural dynamics—how biomolecules move, adapt, and interact over time. Molecular dynamics (MD) simulations provide a powerful atomic-level lens into these processes, revealing mechanisms of function, regulation, and molecular recognition that static structures cannot capture. Yet, extracting meaningful insight from MD data remains difficult. The raw data are massive and multidimensional, and interpretation often demands coding skills, custom workflows, and deep domain expertise. As a result, critical dynamic insights frequently go untapped. This gap limits the translational impact of MD across molecular biology, pharmacology, and structural biophysics. To address this, we developed CATMD—comprehensive analysis toolkit for molecular dynamics, a desktop application that converts raw simulations into 80+ publication-ready figures and metrics from a single run. CATMD consolidates basic analyses such as stability, flexibility, and conformational sampling, while distinguishing itself with advanced modules rarely available in general software. These include residue motion correlations, dynamic cross-correlation matrices, structural state clustering, Markov state modeling, allosteric network analysis, and free-energy landscapes for mapping functional transitions. Interaction analysis tools quantify interaction networks, cooperative or competing contacts, and key residue-ligand associations, while binding interface modules provide energetic decomposition, electrostatics, and solvent occupancy. Dedicated membrane protein analytics assess pore radius, lipid interactions, ion conduction, and membrane deformation—critical for membrane proteins which are predominant drug targets. CATMD’s accessible interface enables non-specialists to run advanced analyses in minutes, guided by plain-language explanations, while experts retain full customization. By removing technical barriers, CATMD transforms massive simulations into clear, actionable insights. It reveals hidden molecular mechanisms, sparks new hypotheses, and accelerates discovery across biology, chemistry, and medicine. In doing so, CATMD unlocks the full potential of MD as a transformative engine for innovation in life sciences.